Genome content of uncultivated marine Roseobacters in the surface ocean
Identifieur interne : 000670 ( Istex/Corpus ); précédent : 000669; suivant : 000671Genome content of uncultivated marine Roseobacters in the surface ocean
Auteurs : Haiwei Luo ; Ari Löytynoja ; Mary Ann MoranSource :
- Environmental Microbiology [ 1462-2912 ] ; 2012-01.
Abstract
Understanding of the ecological roles and evolutionary histories of marine bacterial taxa can be complicated by mismatches in genome content between wild populations and their better‐studied cultured relatives. We used computed patterns of non‐synonymous (amino acid‐altering) nucleotide diversity in marine metagenomic data to provide high‐confidence identification of DNA fragments from uncultivated members of the Roseobacter clade, an abundant taxon of heterotrophic marine bacterioplankton in the world's oceans. Differences in gene stoichiometry in the Global Ocean Survey metagenomic data set compared with 39 sequenced isolates indicated that natural Roseobacter populations differ systematically in several genomic attributes from their cultured representatives, including fewer genes for signal transduction and cell surface modifications but more genes for Sec‐like protein secretion systems, anaplerotic CO2 incorporation, and phosphorus and sulfate uptake. Several of these trends match well with characteristics previously identified as distinguishing r‐ versus K‐selected ecological strategies in bacteria, suggesting that the r‐strategist model assigned to cultured roseobacters may be less applicable to their free‐living oceanic counterparts. The metagenomic Roseobacter DNA fragments revealed several traits with evolutionary histories suggestive of horizontal gene transfer from other marine bacterioplankton taxa or viruses, including pyrophosphatases and glycosylation proteins.
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DOI: 10.1111/j.1462-2920.2011.02528.x
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We used computed patterns of non‐synonymous (amino acid‐altering) nucleotide diversity in marine metagenomic data to provide high‐confidence identification of DNA fragments from uncultivated members of the Roseobacter clade, an abundant taxon of heterotrophic marine bacterioplankton in the world's oceans. Differences in gene stoichiometry in the Global Ocean Survey metagenomic data set compared with 39 sequenced isolates indicated that natural Roseobacter populations differ systematically in several genomic attributes from their cultured representatives, including fewer genes for signal transduction and cell surface modifications but more genes for Sec‐like protein secretion systems, anaplerotic CO2 incorporation, and phosphorus and sulfate uptake. Several of these trends match well with characteristics previously identified as distinguishing r‐ versus K‐selected ecological strategies in bacteria, suggesting that the r‐strategist model assigned to cultured roseobacters may be less applicable to their free‐living oceanic counterparts. The metagenomic Roseobacter DNA fragments revealed several traits with evolutionary histories suggestive of horizontal gene transfer from other marine bacterioplankton taxa or viruses, including pyrophosphatases and glycosylation proteins.</div></front></TEI><istex><corpusName>wiley</corpusName><author><json:item><name>Haiwei Luo</name><affiliations><json:string>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA</json:string></affiliations></json:item><json:item><name>Ari Löytynoja</name><affiliations><json:string>EMBL – European Bioinformatics Institute, Hinxton CB10 1SD, UK</json:string></affiliations></json:item><json:item><name>Mary Ann Moran</name><affiliations><json:string>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA</json:string></affiliations></json:item></author><articleId><json:string>EMI2528</json:string></articleId><language><json:string>eng</json:string></language><originalGenre><json:string>article</json:string></originalGenre><abstract>Understanding of the ecological roles and evolutionary histories of marine bacterial taxa can be complicated by mismatches in genome content between wild populations and their better‐studied cultured relatives. We used computed patterns of non‐synonymous (amino acid‐altering) nucleotide diversity in marine metagenomic data to provide high‐confidence identification of DNA fragments from uncultivated members of the Roseobacter clade, an abundant taxon of heterotrophic marine bacterioplankton in the world's oceans. Differences in gene stoichiometry in the Global Ocean Survey metagenomic data set compared with 39 sequenced isolates indicated that natural Roseobacter populations differ systematically in several genomic attributes from their cultured representatives, including fewer genes for signal transduction and cell surface modifications but more genes for Sec‐like protein secretion systems, anaplerotic CO2 incorporation, and phosphorus and sulfate uptake. Several of these trends match well with characteristics previously identified as distinguishing r‐ versus K‐selected ecological strategies in bacteria, suggesting that the r‐strategist model assigned to cultured roseobacters may be less applicable to their free‐living oceanic counterparts. The metagenomic Roseobacter DNA fragments revealed several traits with evolutionary histories suggestive of horizontal gene transfer from other marine bacterioplankton taxa or viruses, including pyrophosphatases and glycosylation proteins.</abstract><qualityIndicators><score>7.28</score><pdfVersion>1.3</pdfVersion><pdfPageSize>595.275 x 799.371 pts</pdfPageSize><refBibsNative>true</refBibsNative><keywordCount>0</keywordCount><abstractCharCount>1500</abstractCharCount><pdfWordCount>7002</pdfWordCount><pdfCharCount>47689</pdfCharCount><pdfPageCount>11</pdfPageCount><abstractWordCount>190</abstractWordCount></qualityIndicators><title>Genome content of uncultivated marine Roseobacters in the surface ocean</title><genre><json:string>article</json:string></genre><host><volume>14</volume><publisherId><json:string>EMI</json:string></publisherId><pages><total>11</total><last>51</last><first>41</first></pages><issn><json:string>1462-2912</json:string></issn><issue>1</issue><genre><json:string>journal</json:string></genre><language><json:string>unknown</json:string></language><eissn><json:string>1462-2920</json:string></eissn><title>Environmental Microbiology</title><doi><json:string>10.1111/(ISSN)1462-2920</json:string></doi></host><publicationDate>2012</publicationDate><copyrightDate>2012</copyrightDate><doi><json:string>10.1111/j.1462-2920.2011.02528.x</json:string></doi><id>FD28BEBCAE8CCA353020CBBF8897B557B1C7F207</id><score>0.100814484</score><fulltext><json:item><original>true</original><mimetype>application/pdf</mimetype><extension>pdf</extension><uri>https://api.istex.fr/document/FD28BEBCAE8CCA353020CBBF8897B557B1C7F207/fulltext/pdf</uri></json:item><json:item><original>false</original><mimetype>application/zip</mimetype><extension>zip</extension><uri>https://api.istex.fr/document/FD28BEBCAE8CCA353020CBBF8897B557B1C7F207/fulltext/zip</uri></json:item><istex:fulltextTEI uri="https://api.istex.fr/document/FD28BEBCAE8CCA353020CBBF8897B557B1C7F207/fulltext/tei"><teiHeader><fileDesc><titleStmt><title level="a" type="main" xml:lang="en">Genome content of uncultivated marine Roseobacters in the surface ocean</title></titleStmt><publicationStmt><authority>ISTEX</authority><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><availability><p>© 2011 Society for Applied Microbiology and Blackwell Publishing Ltd</p></availability><date>2012</date></publicationStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a" type="main" xml:lang="en">Genome content of uncultivated marine Roseobacters in the surface ocean</title><author xml:id="author-1"><persName><forename type="first">Haiwei</forename><surname>Luo</surname></persName><affiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA</affiliation></author><author xml:id="author-2"><persName><forename type="first">Ari</forename><surname>Löytynoja</surname></persName><affiliation>EMBL – European Bioinformatics Institute, Hinxton CB10 1SD, UK</affiliation></author><author xml:id="author-3"><persName><forename type="first">Mary Ann</forename><surname>Moran</surname></persName><note type="correspondence"><p>Correspondence: E‐mail ; Tel. (+1) 706 542 6481; Fax (+1) 706 542 5888.</p></note><affiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA</affiliation></author></analytic><monogr><title level="j">Environmental Microbiology</title><idno type="pISSN">1462-2912</idno><idno type="eISSN">1462-2920</idno><idno type="DOI">10.1111/(ISSN)1462-2920</idno><imprint><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2012-01"></date><biblScope unit="volume">14</biblScope><biblScope unit="issue">1</biblScope><biblScope unit="page" from="41">41</biblScope><biblScope unit="page" to="51">51</biblScope></imprint></monogr><idno type="istex">FD28BEBCAE8CCA353020CBBF8897B557B1C7F207</idno><idno type="DOI">10.1111/j.1462-2920.2011.02528.x</idno><idno type="ArticleID">EMI2528</idno></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>2012</date></creation><langUsage><language ident="en">en</language></langUsage><abstract xml:lang="en"><p>Understanding of the ecological roles and evolutionary histories of marine bacterial taxa can be complicated by mismatches in genome content between wild populations and their better‐studied cultured relatives. We used computed patterns of non‐synonymous (amino acid‐altering) nucleotide diversity in marine metagenomic data to provide high‐confidence identification of DNA fragments from uncultivated members of the Roseobacter clade, an abundant taxon of heterotrophic marine bacterioplankton in the world's oceans. Differences in gene stoichiometry in the Global Ocean Survey metagenomic data set compared with 39 sequenced isolates indicated that natural Roseobacter populations differ systematically in several genomic attributes from their cultured representatives, including fewer genes for signal transduction and cell surface modifications but more genes for Sec‐like protein secretion systems, anaplerotic CO2 incorporation, and phosphorus and sulfate uptake. Several of these trends match well with characteristics previously identified as distinguishing r‐ versus K‐selected ecological strategies in bacteria, suggesting that the r‐strategist model assigned to cultured roseobacters may be less applicable to their free‐living oceanic counterparts. The metagenomic Roseobacter DNA fragments revealed several traits with evolutionary histories suggestive of horizontal gene transfer from other marine bacterioplankton taxa or viruses, including pyrophosphatases and glycosylation proteins.</p></abstract></profileDesc><revisionDesc><change when="2012-01">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><original>false</original><mimetype>text/plain</mimetype><extension>txt</extension><uri>https://api.istex.fr/document/FD28BEBCAE8CCA353020CBBF8897B557B1C7F207/fulltext/txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Wiley, elements deleted: body"><istex:xmlDeclaration>version="1.0" encoding="UTF-8" standalone="yes"</istex:xmlDeclaration><istex:document><component version="2.0" type="serialArticle" xml:lang="en"><header><publicationMeta level="product"><publisherInfo><publisherName>Blackwell Publishing Ltd</publisherName><publisherLoc>Oxford, UK</publisherLoc></publisherInfo><doi origin="wiley" registered="yes">10.1111/(ISSN)1462-2920</doi><issn type="print">1462-2912</issn><issn type="electronic">1462-2920</issn><idGroup><id type="product" value="EMI"></id><id type="publisherDivision" value="ST"></id></idGroup><titleGroup><title type="main" sort="ENVIRONMENTAL MICROBIOLOGY">Environmental Microbiology</title></titleGroup></publicationMeta><publicationMeta level="part" position="01101"><doi origin="wiley">10.1111/emi.2012.14.issue-1</doi><titleGroup><title type="specialIssueTitle">OMICS Driven Microbial Ecology</title></titleGroup><numberingGroup><numbering type="journalVolume" number="14">14</numbering><numbering type="journalIssue">1</numbering></numberingGroup><coverDate startDate="2012-01">January 2012</coverDate></publicationMeta><publicationMeta level="unit" type="article" position="5" status="forIssue"><doi origin="wiley">10.1111/j.1462-2920.2011.02528.x</doi><idGroup><id type="unit" value="EMI2528"></id></idGroup><countGroup><count type="pageTotal" number="11"></count></countGroup><titleGroup><title type="tocHeading1">Research articles</title></titleGroup><copyright>© 2011 Society for Applied Microbiology and Blackwell Publishing Ltd</copyright><eventGroup><event type="xmlConverted" agent="Converter:BPG_TO_WML3G version:3.1.5 mode:FullText" date="2012-06-13"></event><event type="publishedOnlineEarlyUnpaginated" date="2011-08-19"></event><event type="publishedOnlineFinalForm" date="2012-01-02"></event><event type="firstOnline" date="2011-08-19"></event><event type="xmlConverted" agent="Converter:WILEY_ML3G_TO_WILEY_ML3GV2 version:3.8.8" date="2014-01-24"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:4.3.4 mode:FullText" date="2015-02-25"></event></eventGroup><numberingGroup><numbering type="pageFirst" number="41">41</numbering><numbering type="pageLast" number="51">51</numbering></numberingGroup><correspondenceTo> E‐mail <email>mmoran@uga.edu</email>; Tel. (+1) 706 542 6481; Fax (+1) 706 542 5888. </correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:EMI.EMI2528.pdf"></link></linkGroup></publicationMeta><contentMeta><unparsedEditorialHistory>Received 3 February, 2011; accepted 15 May, 2011.</unparsedEditorialHistory><countGroup><count type="figureTotal" number="4"></count><count type="tableTotal" number="2"></count><count type="formulaTotal" number="0"></count><count type="referenceTotal" number="51"></count><count type="wordTotal" number="7475"></count><count type="linksPubMed" number="0"></count><count type="linksCrossRef" number="0"></count></countGroup><titleGroup><title type="main">Genome content of uncultivated marine <i>Roseobacters</i> in the surface ocean</title><title type="shortAuthors">H. Luo, A. Löytynoja and M. A. Moran</title><title type="short">Genome content of wild <i>Roseobacters</i></title></titleGroup><creators><creator creatorRole="author" xml:id="cr1" affiliationRef="#a1"><personName><givenNames>Haiwei</givenNames><familyName>Luo</familyName></personName></creator><creator creatorRole="author" xml:id="cr2" affiliationRef="#a2"><personName><givenNames>Ari</givenNames><familyName>Löytynoja</familyName></personName></creator><creator creatorRole="author" xml:id="cr3" affiliationRef="#a1" corresponding="yes"><personName><givenNames>Mary Ann</givenNames><familyName>Moran</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="a1" countryCode="US"><unparsedAffiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA</unparsedAffiliation></affiliation><affiliation xml:id="a2" countryCode="GB"><unparsedAffiliation>EMBL – European Bioinformatics Institute, Hinxton CB10 1SD, UK</unparsedAffiliation></affiliation></affiliationGroup><supportingInformation><p><b>Fig. S1.</b> Differential representation of gene families in free‐living oceanic compared with cultured roseobacters (M versus A plot). For the latter, the gene families were directly sampled from all annotated genes in the 39 <i>Roseobacter</i> genomes, rather than only from those linked to a <i>Roseobacter</i> core gene. Families plotting above the line are enriched and those plotting below the line are depleted in the oceanic roseobacters. The colour scheme is the same as for Fig. 1.</p><p><b>Fig. S2.</b> Maximum likelihood phylogeny of the tRNA‐dihydrouridine synthase encoded in the anchor end of JCVI_READ_1172364. The tree was constructed using RAxML 7.0.4 software with the ‘PROTGAMMAWAGF’ model. Values at the nodes show the number of times the clade defined by that node appeared in the 100 bootstrapped data sets.</p><p><b>Fig. S3.</b> Maximum likelihood phylogeny of the Slt transglycosylase encoded in the anchor end of JCVI_READ_926014. The tree was constructed using the method described in Fig. S2.</p><p><b>Fig. S4.</b> Maximum likelihood phylogeny of the pyrophosphatase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2.</p><p><b>Fig. S5.</b> Maximum likelihood phylogeny of the acyltransferase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2.</p><p><b>Table S1.</b> The 348 orthologous genes shared by sequenced 45 marine <i>Alphaproteobacteria</i>. The locus tags in the 45 genomes are given, arranged by gene (row) and organism (column).</p><p><b>Table S2.</b> The 801 orthologous genes shared by sequenced marine <i>Roseobacters</i>. The locus tags in the 39 <i>Roseobacter</i> genomes are given, arranged by gene (row) and organism (column).</p><p><b>Table S3.</b> GOS reads identified by <i>d<sub>N</sub></i> analysis to be of <i>Roseobacter</i> origin.</p><p><b>Table S4.</b> Phylogenetic trees for individual gene families, each of which includes GOS sequences identified by the <i>d<sup>N</sup></i>‐based pipeline and reference genes from the 45 <i>Alphaproteobacteria</i> genomes. <i>Escherichia coli</i> str. K‐12 substr. W3110 was used as an outgroup. Trees were constructed using RAxML.</p><p><b>Table S5.</b> Differential representation of gene families in free‐living oceanic compared with cultured roseobacters. Three simulated metagenomes were constructed with random 2 kb fragments from cultured roseobacters, and each was compared with the oceanic <i>Roseobacter</i> metagenome according to the <i>d<sub>N</sub></i>‐based pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome.</p><p><b>Table S6.</b> GOS sequences identified as <i>Roseobacter</i> by <i>d<sub>N</sub></i> analysis but not by blast best hit analysis.</p><p><b>Table S7.</b> Differential representation of gene families in <i>Roseobacter</i> genomes obtained as HTCC isolates (7 genomes) compared with those obtained by standard culturing methods (32 genomes). Three simulated metagenomes were constructed as random 2 kb fragments from each set of cultured roseobacter genomes and each was compared with the free‐living oceanic <i>Roseobacter</i> metagenome according to the <i>d<sub>N</sub></i> pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Values in the last column (‘Total’) range from 1 (significant in only one replicate simulated metagenome for one genome set) to 6 (significant for all replicate simulated metagenomes for both genome sets).</p><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:14622912:media:emi2528:EMI_2528_sm_FigS1-5"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:14622912:media:emi2528:EMI_2528_sm_tS1"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:14622912:media:emi2528:EMI_2528_sm_tS2"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:14622912:media:emi2528:EMI_2528_sm_tS3"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:14622912:media:emi2528:EMI_2528_sm_tS4"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:14622912:media:emi2528:EMI_2528_sm_tS5"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:14622912:media:emi2528:EMI_2528_sm_tS6"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:14622912:media:emi2528:EMI_2528_sm_tS7"></mediaResource><caption>Supporting info item</caption></supportingInfoItem></supportingInformation><abstractGroup><abstract type="main" xml:lang="en"><title type="main">Summary</title><p>Understanding of the ecological roles and evolutionary histories of marine bacterial taxa can be complicated by mismatches in genome content between wild populations and their better‐studied cultured relatives. We used computed patterns of non‐synonymous (amino acid‐altering) nucleotide diversity in marine metagenomic data to provide high‐confidence identification of DNA fragments from uncultivated members of the <i>Roseobacter</i> clade, an abundant taxon of heterotrophic marine bacterioplankton in the world's oceans. Differences in gene stoichiometry in the Global Ocean Survey metagenomic data set compared with 39 sequenced isolates indicated that natural <i>Roseobacter</i> populations differ systematically in several genomic attributes from their cultured representatives, including fewer genes for signal transduction and cell surface modifications but more genes for Sec‐like protein secretion systems, anaplerotic CO<sub>2</sub> incorporation, and phosphorus and sulfate uptake. Several of these trends match well with characteristics previously identified as distinguishing r‐ versus K‐selected ecological strategies in bacteria, suggesting that the r‐strategist model assigned to cultured roseobacters may be less applicable to their free‐living oceanic counterparts. The metagenomic <i>Roseobacter</i> DNA fragments revealed several traits with evolutionary histories suggestive of horizontal gene transfer from other marine bacterioplankton taxa or viruses, including pyrophosphatases and glycosylation proteins.</p></abstract></abstractGroup></contentMeta></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Genome content of uncultivated marine Roseobacters in the surface ocean</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>Genome content of wild Roseobacters</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Genome content of uncultivated marine Roseobacters in the surface ocean</title></titleInfo><name type="personal"><namePart type="given">Haiwei</namePart><namePart type="family">Luo</namePart><affiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Ari</namePart><namePart type="family">Löytynoja</namePart><affiliation>EMBL – European Bioinformatics Institute, Hinxton CB10 1SD, UK</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Mary Ann</namePart><namePart type="family">Moran</namePart><affiliation>Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA</affiliation><description>Correspondence: E‐mail ; Tel. (+1) 706 542 6481; Fax (+1) 706 542 5888.</description><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="article"></genre><originInfo><publisher>Blackwell Publishing Ltd</publisher><place><placeTerm type="text">Oxford, UK</placeTerm></place><dateIssued encoding="w3cdtf">2012-01</dateIssued><edition>Received 3 February, 2011; accepted 15 May, 2011.</edition><copyrightDate encoding="w3cdtf">2012</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType><extent unit="figures">4</extent><extent unit="tables">2</extent><extent unit="references">51</extent><extent unit="words">7475</extent></physicalDescription><abstract lang="en">Understanding of the ecological roles and evolutionary histories of marine bacterial taxa can be complicated by mismatches in genome content between wild populations and their better‐studied cultured relatives. We used computed patterns of non‐synonymous (amino acid‐altering) nucleotide diversity in marine metagenomic data to provide high‐confidence identification of DNA fragments from uncultivated members of the Roseobacter clade, an abundant taxon of heterotrophic marine bacterioplankton in the world's oceans. Differences in gene stoichiometry in the Global Ocean Survey metagenomic data set compared with 39 sequenced isolates indicated that natural Roseobacter populations differ systematically in several genomic attributes from their cultured representatives, including fewer genes for signal transduction and cell surface modifications but more genes for Sec‐like protein secretion systems, anaplerotic CO2 incorporation, and phosphorus and sulfate uptake. Several of these trends match well with characteristics previously identified as distinguishing r‐ versus K‐selected ecological strategies in bacteria, suggesting that the r‐strategist model assigned to cultured roseobacters may be less applicable to their free‐living oceanic counterparts. The metagenomic Roseobacter DNA fragments revealed several traits with evolutionary histories suggestive of horizontal gene transfer from other marine bacterioplankton taxa or viruses, including pyrophosphatases and glycosylation proteins.</abstract><relatedItem type="host"><titleInfo><title>Environmental Microbiology</title></titleInfo><genre type="journal">journal</genre><note type="content"> Fig. S1. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters (M versus A plot). For the latter, the gene families were directly sampled from all annotated genes in the 39 Roseobacter genomes, rather than only from those linked to a Roseobacter core gene. Families plotting above the line are enriched and those plotting below the line are depleted in the oceanic roseobacters. The colour scheme is the same as for Fig. 1. Fig. S2. Maximum likelihood phylogeny of the tRNA‐dihydrouridine synthase encoded in the anchor end of JCVI_READ_1172364. The tree was constructed using RAxML 7.0.4 software with the ‘PROTGAMMAWAGF’ model. Values at the nodes show the number of times the clade defined by that node appeared in the 100 bootstrapped data sets. Fig. S3. Maximum likelihood phylogeny of the Slt transglycosylase encoded in the anchor end of JCVI_READ_926014. The tree was constructed using the method described in Fig. S2. Fig. S4. Maximum likelihood phylogeny of the pyrophosphatase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Fig. S5. Maximum likelihood phylogeny of the acyltransferase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Table S1. The 348 orthologous genes shared by sequenced 45 marine Alphaproteobacteria. The locus tags in the 45 genomes are given, arranged by gene (row) and organism (column). Table S2. The 801 orthologous genes shared by sequenced marine Roseobacters. The locus tags in the 39 Roseobacter genomes are given, arranged by gene (row) and organism (column). Table S3. GOS reads identified by dN analysis to be of Roseobacter origin. Table S4. Phylogenetic trees for individual gene families, each of which includes GOS sequences identified by the dN ‐based pipeline and reference genes from the 45 Alphaproteobacteria genomes. Escherichia coli str. K‐12 substr. W3110 was used as an outgroup. Trees were constructed using RAxML. Table S5. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters. Three simulated metagenomes were constructed with random 2 kb fragments from cultured roseobacters, and each was compared with the oceanic Roseobacter metagenome according to the dN ‐based pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Table S6. GOS sequences identified as Roseobacter by dN analysis but not by blast best hit analysis. Table S7. Differential representation of gene families in Roseobacter genomes obtained as HTCC isolates (7 genomes) compared with those obtained by standard culturing methods (32 genomes). Three simulated metagenomes were constructed as random 2 kb fragments from each set of cultured roseobacter genomes and each was compared with the free‐living oceanic Roseobacter metagenome according to the dN pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Values in the last column (‘Total’) range from 1 (significant in only one replicate simulated metagenome for one genome set) to 6 (significant for all replicate simulated metagenomes for both genome sets). Fig. S1. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters (M versus A plot). For the latter, the gene families were directly sampled from all annotated genes in the 39 Roseobacter genomes, rather than only from those linked to a Roseobacter core gene. Families plotting above the line are enriched and those plotting below the line are depleted in the oceanic roseobacters. The colour scheme is the same as for Fig. 1. Fig. S2. Maximum likelihood phylogeny of the tRNA‐dihydrouridine synthase encoded in the anchor end of JCVI_READ_1172364. The tree was constructed using RAxML 7.0.4 software with the ‘PROTGAMMAWAGF’ model. Values at the nodes show the number of times the clade defined by that node appeared in the 100 bootstrapped data sets. Fig. S3. Maximum likelihood phylogeny of the Slt transglycosylase encoded in the anchor end of JCVI_READ_926014. The tree was constructed using the method described in Fig. S2. Fig. S4. Maximum likelihood phylogeny of the pyrophosphatase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Fig. S5. Maximum likelihood phylogeny of the acyltransferase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Table S1. The 348 orthologous genes shared by sequenced 45 marine Alphaproteobacteria. The locus tags in the 45 genomes are given, arranged by gene (row) and organism (column). Table S2. The 801 orthologous genes shared by sequenced marine Roseobacters. The locus tags in the 39 Roseobacter genomes are given, arranged by gene (row) and organism (column). Table S3. GOS reads identified by dN analysis to be of Roseobacter origin. Table S4. Phylogenetic trees for individual gene families, each of which includes GOS sequences identified by the dN ‐based pipeline and reference genes from the 45 Alphaproteobacteria genomes. Escherichia coli str. K‐12 substr. W3110 was used as an outgroup. Trees were constructed using RAxML. Table S5. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters. Three simulated metagenomes were constructed with random 2 kb fragments from cultured roseobacters, and each was compared with the oceanic Roseobacter metagenome according to the dN ‐based pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Table S6. GOS sequences identified as Roseobacter by dN analysis but not by blast best hit analysis. Table S7. Differential representation of gene families in Roseobacter genomes obtained as HTCC isolates (7 genomes) compared with those obtained by standard culturing methods (32 genomes). Three simulated metagenomes were constructed as random 2 kb fragments from each set of cultured roseobacter genomes and each was compared with the free‐living oceanic Roseobacter metagenome according to the dN pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Values in the last column (‘Total’) range from 1 (significant in only one replicate simulated metagenome for one genome set) to 6 (significant for all replicate simulated metagenomes for both genome sets). Fig. S1. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters (M versus A plot). For the latter, the gene families were directly sampled from all annotated genes in the 39 Roseobacter genomes, rather than only from those linked to a Roseobacter core gene. Families plotting above the line are enriched and those plotting below the line are depleted in the oceanic roseobacters. The colour scheme is the same as for Fig. 1. Fig. S2. Maximum likelihood phylogeny of the tRNA‐dihydrouridine synthase encoded in the anchor end of JCVI_READ_1172364. The tree was constructed using RAxML 7.0.4 software with the ‘PROTGAMMAWAGF’ model. Values at the nodes show the number of times the clade defined by that node appeared in the 100 bootstrapped data sets. Fig. S3. Maximum likelihood phylogeny of the Slt transglycosylase encoded in the anchor end of JCVI_READ_926014. The tree was constructed using the method described in Fig. S2. Fig. S4. Maximum likelihood phylogeny of the pyrophosphatase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Fig. S5. Maximum likelihood phylogeny of the acyltransferase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Table S1. The 348 orthologous genes shared by sequenced 45 marine Alphaproteobacteria. The locus tags in the 45 genomes are given, arranged by gene (row) and organism (column). Table S2. The 801 orthologous genes shared by sequenced marine Roseobacters. The locus tags in the 39 Roseobacter genomes are given, arranged by gene (row) and organism (column). Table S3. GOS reads identified by dN analysis to be of Roseobacter origin. Table S4. Phylogenetic trees for individual gene families, each of which includes GOS sequences identified by the dN ‐based pipeline and reference genes from the 45 Alphaproteobacteria genomes. Escherichia coli str. K‐12 substr. W3110 was used as an outgroup. Trees were constructed using RAxML. Table S5. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters. Three simulated metagenomes were constructed with random 2 kb fragments from cultured roseobacters, and each was compared with the oceanic Roseobacter metagenome according to the dN ‐based pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Table S6. GOS sequences identified as Roseobacter by dN analysis but not by blast best hit analysis. Table S7. Differential representation of gene families in Roseobacter genomes obtained as HTCC isolates (7 genomes) compared with those obtained by standard culturing methods (32 genomes). Three simulated metagenomes were constructed as random 2 kb fragments from each set of cultured roseobacter genomes and each was compared with the free‐living oceanic Roseobacter metagenome according to the dN pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Values in the last column (‘Total’) range from 1 (significant in only one replicate simulated metagenome for one genome set) to 6 (significant for all replicate simulated metagenomes for both genome sets). Fig. S1. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters (M versus A plot). For the latter, the gene families were directly sampled from all annotated genes in the 39 Roseobacter genomes, rather than only from those linked to a Roseobacter core gene. Families plotting above the line are enriched and those plotting below the line are depleted in the oceanic roseobacters. The colour scheme is the same as for Fig. 1. Fig. S2. Maximum likelihood phylogeny of the tRNA‐dihydrouridine synthase encoded in the anchor end of JCVI_READ_1172364. The tree was constructed using RAxML 7.0.4 software with the ‘PROTGAMMAWAGF’ model. Values at the nodes show the number of times the clade defined by that node appeared in the 100 bootstrapped data sets. Fig. S3. Maximum likelihood phylogeny of the Slt transglycosylase encoded in the anchor end of JCVI_READ_926014. The tree was constructed using the method described in Fig. S2. Fig. S4. Maximum likelihood phylogeny of the pyrophosphatase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Fig. S5. Maximum likelihood phylogeny of the acyltransferase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Table S1. The 348 orthologous genes shared by sequenced 45 marine Alphaproteobacteria. The locus tags in the 45 genomes are given, arranged by gene (row) and organism (column). Table S2. The 801 orthologous genes shared by sequenced marine Roseobacters. The locus tags in the 39 Roseobacter genomes are given, arranged by gene (row) and organism (column). Table S3. GOS reads identified by dN analysis to be of Roseobacter origin. Table S4. Phylogenetic trees for individual gene families, each of which includes GOS sequences identified by the dN ‐based pipeline and reference genes from the 45 Alphaproteobacteria genomes. Escherichia coli str. K‐12 substr. W3110 was used as an outgroup. Trees were constructed using RAxML. Table S5. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters. Three simulated metagenomes were constructed with random 2 kb fragments from cultured roseobacters, and each was compared with the oceanic Roseobacter metagenome according to the dN ‐based pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Table S6. GOS sequences identified as Roseobacter by dN analysis but not by blast best hit analysis. Table S7. Differential representation of gene families in Roseobacter genomes obtained as HTCC isolates (7 genomes) compared with those obtained by standard culturing methods (32 genomes). Three simulated metagenomes were constructed as random 2 kb fragments from each set of cultured roseobacter genomes and each was compared with the free‐living oceanic Roseobacter metagenome according to the dN pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Values in the last column (‘Total’) range from 1 (significant in only one replicate simulated metagenome for one genome set) to 6 (significant for all replicate simulated metagenomes for both genome sets). Fig. S1. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters (M versus A plot). For the latter, the gene families were directly sampled from all annotated genes in the 39 Roseobacter genomes, rather than only from those linked to a Roseobacter core gene. Families plotting above the line are enriched and those plotting below the line are depleted in the oceanic roseobacters. The colour scheme is the same as for Fig. 1. Fig. S2. Maximum likelihood phylogeny of the tRNA‐dihydrouridine synthase encoded in the anchor end of JCVI_READ_1172364. The tree was constructed using RAxML 7.0.4 software with the ‘PROTGAMMAWAGF’ model. Values at the nodes show the number of times the clade defined by that node appeared in the 100 bootstrapped data sets. Fig. S3. Maximum likelihood phylogeny of the Slt transglycosylase encoded in the anchor end of JCVI_READ_926014. The tree was constructed using the method described in Fig. S2. Fig. S4. Maximum likelihood phylogeny of the pyrophosphatase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Fig. S5. Maximum likelihood phylogeny of the acyltransferase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Table S1. The 348 orthologous genes shared by sequenced 45 marine Alphaproteobacteria. The locus tags in the 45 genomes are given, arranged by gene (row) and organism (column). Table S2. The 801 orthologous genes shared by sequenced marine Roseobacters. The locus tags in the 39 Roseobacter genomes are given, arranged by gene (row) and organism (column). Table S3. GOS reads identified by dN analysis to be of Roseobacter origin. Table S4. Phylogenetic trees for individual gene families, each of which includes GOS sequences identified by the dN ‐based pipeline and reference genes from the 45 Alphaproteobacteria genomes. Escherichia coli str. K‐12 substr. W3110 was used as an outgroup. Trees were constructed using RAxML. Table S5. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters. Three simulated metagenomes were constructed with random 2 kb fragments from cultured roseobacters, and each was compared with the oceanic Roseobacter metagenome according to the dN ‐based pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Table S6. GOS sequences identified as Roseobacter by dN analysis but not by blast best hit analysis. Table S7. Differential representation of gene families in Roseobacter genomes obtained as HTCC isolates (7 genomes) compared with those obtained by standard culturing methods (32 genomes). Three simulated metagenomes were constructed as random 2 kb fragments from each set of cultured roseobacter genomes and each was compared with the free‐living oceanic Roseobacter metagenome according to the dN pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Values in the last column (‘Total’) range from 1 (significant in only one replicate simulated metagenome for one genome set) to 6 (significant for all replicate simulated metagenomes for both genome sets). Fig. S1. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters (M versus A plot). For the latter, the gene families were directly sampled from all annotated genes in the 39 Roseobacter genomes, rather than only from those linked to a Roseobacter core gene. Families plotting above the line are enriched and those plotting below the line are depleted in the oceanic roseobacters. The colour scheme is the same as for Fig. 1. Fig. S2. Maximum likelihood phylogeny of the tRNA‐dihydrouridine synthase encoded in the anchor end of JCVI_READ_1172364. The tree was constructed using RAxML 7.0.4 software with the ‘PROTGAMMAWAGF’ model. Values at the nodes show the number of times the clade defined by that node appeared in the 100 bootstrapped data sets. Fig. S3. Maximum likelihood phylogeny of the Slt transglycosylase encoded in the anchor end of JCVI_READ_926014. The tree was constructed using the method described in Fig. S2. Fig. S4. Maximum likelihood phylogeny of the pyrophosphatase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Fig. S5. Maximum likelihood phylogeny of the acyltransferase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Table S1. The 348 orthologous genes shared by sequenced 45 marine Alphaproteobacteria. The locus tags in the 45 genomes are given, arranged by gene (row) and organism (column). Table S2. The 801 orthologous genes shared by sequenced marine Roseobacters. The locus tags in the 39 Roseobacter genomes are given, arranged by gene (row) and organism (column). Table S3. GOS reads identified by dN analysis to be of Roseobacter origin. Table S4. Phylogenetic trees for individual gene families, each of which includes GOS sequences identified by the dN ‐based pipeline and reference genes from the 45 Alphaproteobacteria genomes. Escherichia coli str. K‐12 substr. W3110 was used as an outgroup. Trees were constructed using RAxML. Table S5. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters. Three simulated metagenomes were constructed with random 2 kb fragments from cultured roseobacters, and each was compared with the oceanic Roseobacter metagenome according to the dN ‐based pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Table S6. GOS sequences identified as Roseobacter by dN analysis but not by blast best hit analysis. Table S7. Differential representation of gene families in Roseobacter genomes obtained as HTCC isolates (7 genomes) compared with those obtained by standard culturing methods (32 genomes). Three simulated metagenomes were constructed as random 2 kb fragments from each set of cultured roseobacter genomes and each was compared with the free‐living oceanic Roseobacter metagenome according to the dN pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Values in the last column (‘Total’) range from 1 (significant in only one replicate simulated metagenome for one genome set) to 6 (significant for all replicate simulated metagenomes for both genome sets). Fig. S1. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters (M versus A plot). For the latter, the gene families were directly sampled from all annotated genes in the 39 Roseobacter genomes, rather than only from those linked to a Roseobacter core gene. Families plotting above the line are enriched and those plotting below the line are depleted in the oceanic roseobacters. The colour scheme is the same as for Fig. 1. Fig. S2. Maximum likelihood phylogeny of the tRNA‐dihydrouridine synthase encoded in the anchor end of JCVI_READ_1172364. The tree was constructed using RAxML 7.0.4 software with the ‘PROTGAMMAWAGF’ model. Values at the nodes show the number of times the clade defined by that node appeared in the 100 bootstrapped data sets. Fig. S3. Maximum likelihood phylogeny of the Slt transglycosylase encoded in the anchor end of JCVI_READ_926014. The tree was constructed using the method described in Fig. S2. Fig. S4. Maximum likelihood phylogeny of the pyrophosphatase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Fig. S5. Maximum likelihood phylogeny of the acyltransferase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Table S1. The 348 orthologous genes shared by sequenced 45 marine Alphaproteobacteria. The locus tags in the 45 genomes are given, arranged by gene (row) and organism (column). Table S2. The 801 orthologous genes shared by sequenced marine Roseobacters. The locus tags in the 39 Roseobacter genomes are given, arranged by gene (row) and organism (column). Table S3. GOS reads identified by dN analysis to be of Roseobacter origin. Table S4. Phylogenetic trees for individual gene families, each of which includes GOS sequences identified by the dN ‐based pipeline and reference genes from the 45 Alphaproteobacteria genomes. Escherichia coli str. K‐12 substr. W3110 was used as an outgroup. Trees were constructed using RAxML. Table S5. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters. Three simulated metagenomes were constructed with random 2 kb fragments from cultured roseobacters, and each was compared with the oceanic Roseobacter metagenome according to the dN ‐based pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Table S6. GOS sequences identified as Roseobacter by dN analysis but not by blast best hit analysis. Table S7. Differential representation of gene families in Roseobacter genomes obtained as HTCC isolates (7 genomes) compared with those obtained by standard culturing methods (32 genomes). Three simulated metagenomes were constructed as random 2 kb fragments from each set of cultured roseobacter genomes and each was compared with the free‐living oceanic Roseobacter metagenome according to the dN pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Values in the last column (‘Total’) range from 1 (significant in only one replicate simulated metagenome for one genome set) to 6 (significant for all replicate simulated metagenomes for both genome sets). Fig. S1. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters (M versus A plot). For the latter, the gene families were directly sampled from all annotated genes in the 39 Roseobacter genomes, rather than only from those linked to a Roseobacter core gene. Families plotting above the line are enriched and those plotting below the line are depleted in the oceanic roseobacters. The colour scheme is the same as for Fig. 1. Fig. S2. Maximum likelihood phylogeny of the tRNA‐dihydrouridine synthase encoded in the anchor end of JCVI_READ_1172364. The tree was constructed using RAxML 7.0.4 software with the ‘PROTGAMMAWAGF’ model. Values at the nodes show the number of times the clade defined by that node appeared in the 100 bootstrapped data sets. Fig. S3. Maximum likelihood phylogeny of the Slt transglycosylase encoded in the anchor end of JCVI_READ_926014. The tree was constructed using the method described in Fig. S2. Fig. S4. Maximum likelihood phylogeny of the pyrophosphatase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Fig. S5. Maximum likelihood phylogeny of the acyltransferase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Table S1. The 348 orthologous genes shared by sequenced 45 marine Alphaproteobacteria. The locus tags in the 45 genomes are given, arranged by gene (row) and organism (column). Table S2. The 801 orthologous genes shared by sequenced marine Roseobacters. The locus tags in the 39 Roseobacter genomes are given, arranged by gene (row) and organism (column). Table S3. GOS reads identified by dN analysis to be of Roseobacter origin. Table S4. Phylogenetic trees for individual gene families, each of which includes GOS sequences identified by the dN ‐based pipeline and reference genes from the 45 Alphaproteobacteria genomes. Escherichia coli str. K‐12 substr. W3110 was used as an outgroup. Trees were constructed using RAxML. Table S5. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters. Three simulated metagenomes were constructed with random 2 kb fragments from cultured roseobacters, and each was compared with the oceanic Roseobacter metagenome according to the dN ‐based pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Table S6. GOS sequences identified as Roseobacter by dN analysis but not by blast best hit analysis. Table S7. Differential representation of gene families in Roseobacter genomes obtained as HTCC isolates (7 genomes) compared with those obtained by standard culturing methods (32 genomes). Three simulated metagenomes were constructed as random 2 kb fragments from each set of cultured roseobacter genomes and each was compared with the free‐living oceanic Roseobacter metagenome according to the dN pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Values in the last column (‘Total’) range from 1 (significant in only one replicate simulated metagenome for one genome set) to 6 (significant for all replicate simulated metagenomes for both genome sets). Fig. S1. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters (M versus A plot). For the latter, the gene families were directly sampled from all annotated genes in the 39 Roseobacter genomes, rather than only from those linked to a Roseobacter core gene. Families plotting above the line are enriched and those plotting below the line are depleted in the oceanic roseobacters. The colour scheme is the same as for Fig. 1. Fig. S2. Maximum likelihood phylogeny of the tRNA‐dihydrouridine synthase encoded in the anchor end of JCVI_READ_1172364. The tree was constructed using RAxML 7.0.4 software with the ‘PROTGAMMAWAGF’ model. Values at the nodes show the number of times the clade defined by that node appeared in the 100 bootstrapped data sets. Fig. S3. Maximum likelihood phylogeny of the Slt transglycosylase encoded in the anchor end of JCVI_READ_926014. The tree was constructed using the method described in Fig. S2. Fig. S4. Maximum likelihood phylogeny of the pyrophosphatase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Fig. S5. Maximum likelihood phylogeny of the acyltransferase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Table S1. The 348 orthologous genes shared by sequenced 45 marine Alphaproteobacteria. The locus tags in the 45 genomes are given, arranged by gene (row) and organism (column). Table S2. The 801 orthologous genes shared by sequenced marine Roseobacters. The locus tags in the 39 Roseobacter genomes are given, arranged by gene (row) and organism (column). Table S3. GOS reads identified by dN analysis to be of Roseobacter origin. Table S4. Phylogenetic trees for individual gene families, each of which includes GOS sequences identified by the dN ‐based pipeline and reference genes from the 45 Alphaproteobacteria genomes. Escherichia coli str. K‐12 substr. W3110 was used as an outgroup. Trees were constructed using RAxML. Table S5. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters. Three simulated metagenomes were constructed with random 2 kb fragments from cultured roseobacters, and each was compared with the oceanic Roseobacter metagenome according to the dN ‐based pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Table S6. GOS sequences identified as Roseobacter by dN analysis but not by blast best hit analysis. Table S7. Differential representation of gene families in Roseobacter genomes obtained as HTCC isolates (7 genomes) compared with those obtained by standard culturing methods (32 genomes). Three simulated metagenomes were constructed as random 2 kb fragments from each set of cultured roseobacter genomes and each was compared with the free‐living oceanic Roseobacter metagenome according to the dN pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Values in the last column (‘Total’) range from 1 (significant in only one replicate simulated metagenome for one genome set) to 6 (significant for all replicate simulated metagenomes for both genome sets). Fig. S1. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters (M versus A plot). For the latter, the gene families were directly sampled from all annotated genes in the 39 Roseobacter genomes, rather than only from those linked to a Roseobacter core gene. Families plotting above the line are enriched and those plotting below the line are depleted in the oceanic roseobacters. The colour scheme is the same as for Fig. 1. Fig. S2. Maximum likelihood phylogeny of the tRNA‐dihydrouridine synthase encoded in the anchor end of JCVI_READ_1172364. The tree was constructed using RAxML 7.0.4 software with the ‘PROTGAMMAWAGF’ model. Values at the nodes show the number of times the clade defined by that node appeared in the 100 bootstrapped data sets. Fig. S3. Maximum likelihood phylogeny of the Slt transglycosylase encoded in the anchor end of JCVI_READ_926014. The tree was constructed using the method described in Fig. S2. Fig. S4. Maximum likelihood phylogeny of the pyrophosphatase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Fig. S5. Maximum likelihood phylogeny of the acyltransferase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Table S1. The 348 orthologous genes shared by sequenced 45 marine Alphaproteobacteria. The locus tags in the 45 genomes are given, arranged by gene (row) and organism (column). Table S2. The 801 orthologous genes shared by sequenced marine Roseobacters. The locus tags in the 39 Roseobacter genomes are given, arranged by gene (row) and organism (column). Table S3. GOS reads identified by dN analysis to be of Roseobacter origin. Table S4. Phylogenetic trees for individual gene families, each of which includes GOS sequences identified by the dN ‐based pipeline and reference genes from the 45 Alphaproteobacteria genomes. Escherichia coli str. K‐12 substr. W3110 was used as an outgroup. Trees were constructed using RAxML. Table S5. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters. Three simulated metagenomes were constructed with random 2 kb fragments from cultured roseobacters, and each was compared with the oceanic Roseobacter metagenome according to the dN ‐based pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Table S6. GOS sequences identified as Roseobacter by dN analysis but not by blast best hit analysis. Table S7. Differential representation of gene families in Roseobacter genomes obtained as HTCC isolates (7 genomes) compared with those obtained by standard culturing methods (32 genomes). Three simulated metagenomes were constructed as random 2 kb fragments from each set of cultured roseobacter genomes and each was compared with the free‐living oceanic Roseobacter metagenome according to the dN pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Values in the last column (‘Total’) range from 1 (significant in only one replicate simulated metagenome for one genome set) to 6 (significant for all replicate simulated metagenomes for both genome sets). Fig. S1. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters (M versus A plot). For the latter, the gene families were directly sampled from all annotated genes in the 39 Roseobacter genomes, rather than only from those linked to a Roseobacter core gene. Families plotting above the line are enriched and those plotting below the line are depleted in the oceanic roseobacters. The colour scheme is the same as for Fig. 1. Fig. S2. Maximum likelihood phylogeny of the tRNA‐dihydrouridine synthase encoded in the anchor end of JCVI_READ_1172364. The tree was constructed using RAxML 7.0.4 software with the ‘PROTGAMMAWAGF’ model. Values at the nodes show the number of times the clade defined by that node appeared in the 100 bootstrapped data sets. Fig. S3. Maximum likelihood phylogeny of the Slt transglycosylase encoded in the anchor end of JCVI_READ_926014. The tree was constructed using the method described in Fig. S2. Fig. S4. Maximum likelihood phylogeny of the pyrophosphatase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Fig. S5. Maximum likelihood phylogeny of the acyltransferase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Table S1. The 348 orthologous genes shared by sequenced 45 marine Alphaproteobacteria. The locus tags in the 45 genomes are given, arranged by gene (row) and organism (column). Table S2. The 801 orthologous genes shared by sequenced marine Roseobacters. The locus tags in the 39 Roseobacter genomes are given, arranged by gene (row) and organism (column). Table S3. GOS reads identified by dN analysis to be of Roseobacter origin. Table S4. Phylogenetic trees for individual gene families, each of which includes GOS sequences identified by the dN ‐based pipeline and reference genes from the 45 Alphaproteobacteria genomes. Escherichia coli str. K‐12 substr. W3110 was used as an outgroup. Trees were constructed using RAxML. Table S5. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters. Three simulated metagenomes were constructed with random 2 kb fragments from cultured roseobacters, and each was compared with the oceanic Roseobacter metagenome according to the dN ‐based pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Table S6. GOS sequences identified as Roseobacter by dN analysis but not by blast best hit analysis. Table S7. Differential representation of gene families in Roseobacter genomes obtained as HTCC isolates (7 genomes) compared with those obtained by standard culturing methods (32 genomes). Three simulated metagenomes were constructed as random 2 kb fragments from each set of cultured roseobacter genomes and each was compared with the free‐living oceanic Roseobacter metagenome according to the dN pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Values in the last column (‘Total’) range from 1 (significant in only one replicate simulated metagenome for one genome set) to 6 (significant for all replicate simulated metagenomes for both genome sets). Fig. S1. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters (M versus A plot). For the latter, the gene families were directly sampled from all annotated genes in the 39 Roseobacter genomes, rather than only from those linked to a Roseobacter core gene. Families plotting above the line are enriched and those plotting below the line are depleted in the oceanic roseobacters. The colour scheme is the same as for Fig. 1. Fig. S2. Maximum likelihood phylogeny of the tRNA‐dihydrouridine synthase encoded in the anchor end of JCVI_READ_1172364. The tree was constructed using RAxML 7.0.4 software with the ‘PROTGAMMAWAGF’ model. Values at the nodes show the number of times the clade defined by that node appeared in the 100 bootstrapped data sets. Fig. S3. Maximum likelihood phylogeny of the Slt transglycosylase encoded in the anchor end of JCVI_READ_926014. The tree was constructed using the method described in Fig. S2. Fig. S4. Maximum likelihood phylogeny of the pyrophosphatase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Fig. S5. Maximum likelihood phylogeny of the acyltransferase encoded in the mate read of JCVI_READ_1172365. The tree was constructed using the method described in Fig. S2. Table S1. The 348 orthologous genes shared by sequenced 45 marine Alphaproteobacteria. The locus tags in the 45 genomes are given, arranged by gene (row) and organism (column). Table S2. The 801 orthologous genes shared by sequenced marine Roseobacters. The locus tags in the 39 Roseobacter genomes are given, arranged by gene (row) and organism (column). Table S3. GOS reads identified by dN analysis to be of Roseobacter origin. Table S4. Phylogenetic trees for individual gene families, each of which includes GOS sequences identified by the dN ‐based pipeline and reference genes from the 45 Alphaproteobacteria genomes. Escherichia coli str. K‐12 substr. W3110 was used as an outgroup. Trees were constructed using RAxML. Table S5. Differential representation of gene families in free‐living oceanic compared with cultured roseobacters. Three simulated metagenomes were constructed with random 2 kb fragments from cultured roseobacters, and each was compared with the oceanic Roseobacter metagenome according to the dN ‐based pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Table S6. GOS sequences identified as Roseobacter by dN analysis but not by blast best hit analysis. Table S7. Differential representation of gene families in Roseobacter genomes obtained as HTCC isolates (7 genomes) compared with those obtained by standard culturing methods (32 genomes). Three simulated metagenomes were constructed as random 2 kb fragments from each set of cultured roseobacter genomes and each was compared with the free‐living oceanic Roseobacter metagenome according to the dN pipeline. A ‘1’ indicates that the gene family was significantly different between the oceanic and cultured metagenome. Values in the last column (‘Total’) range from 1 (significant in only one replicate simulated metagenome for one genome set) to 6 (significant for all replicate simulated metagenomes for both genome sets).Supporting Info Item: Supporting info item - Supporting info item - Supporting info item - Supporting info item - Supporting info item - Supporting info item - Supporting info item - Supporting info item - </note><identifier type="ISSN">1462-2912</identifier><identifier type="eISSN">1462-2920</identifier><identifier type="DOI">10.1111/(ISSN)1462-2920</identifier><identifier type="PublisherID">EMI</identifier><part><date>2012</date><detail type="title"><title>OMICS Driven Microbial Ecology</title></detail><detail type="volume"><caption>vol.</caption><number>14</number></detail><detail type="issue"><caption>no.</caption><number>1</number></detail><extent unit="pages"><start>41</start><end>51</end><total>11</total></extent></part></relatedItem><identifier type="istex">FD28BEBCAE8CCA353020CBBF8897B557B1C7F207</identifier><identifier type="DOI">10.1111/j.1462-2920.2011.02528.x</identifier><identifier type="ArticleID">EMI2528</identifier><accessCondition type="use and reproduction" contentType="copyright">© 2011 Society for Applied Microbiology and Blackwell Publishing Ltd</accessCondition><recordInfo><recordContentSource>WILEY</recordContentSource><recordOrigin>Blackwell Publishing Ltd</recordOrigin></recordInfo></mods></metadata><enrichments><json:item><type>multicat</type><uri>https://api.istex.fr/document/FD28BEBCAE8CCA353020CBBF8897B557B1C7F207/enrichments/multicat</uri></json:item></enrichments><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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